jimmayxu

arboreto

A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.

bbknn

Batch balanced KNN

Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference

biotransfer

Machine learning-driven antibody design

Blog

damtp-unix-intro

Intro materials for mphil students to get started on damtp machines.

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

INVASE

IINVASE: Instance-wise Variable Selection using Neural Networks - 2019 ICLR

KPNN

Knowledge-primed neural networks

L2X

pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis

scRACING

scRNAseq_clustering_comparison

A study to compare methods for clustering of scRNA-seq data

scVAE

Deep learning for single-cell transcript counts

scVI

Deep generative modeling for single-cell transcriptomics

SERGIO

A simulator for single-cell expression data guided by gene regulatory networks

SIMLR

Implementations in both Matlab and R of the SIMLR method. The manuscript of the method is available at: https://www.nature.com/articles/nmeth.4207

splatter

Simple simulation of single-cell RNA sequencing data

Tutorial-in-Dimensionality-Reduction-Methods

y-intercept-Zhihan_Xu